Reanalysis RNA-Seq (GSE147507)
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Summary of Data/ Analysis
- 20 Samples total
- source cell lines - A549 ( Lung Adenocarcinoma), NHBE ( Primary Human Bronchial Lung Epithelium Cells )
- Raw Fastq Downloaded from GEO:GSE147507
- Aligned to hg38 using STAR
- Raw Counts using HTSeq
- Normalized Expression FPKM
Infected with 3 strains:
- SARS-Cov2 - US/WA1 Strain
- Respiratory syncytial virus(RSV)
- Influenza A (IAV)
Multiplicity of infection (MOI) variables - [ ratio of virions to target cells ]
- SAR-Cov2 in NHBE - MOI 2.0
- SAR-Cov2 in A549 - MOI 0.2
- RSV in A549 - MOI 15
- IAV in A549 - MOI 5
Differential Expression
- A549 : SARS-CoV2 (MOI 0.2) vs. Cov2-Mock
- NHBE : SARS-CoV2 (MOI 2) vs. Cov2-Mock
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Sample Annotation
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Principle Component Analysis
QC Genes
A549 Comparisons
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Differential Expression Analysis
- Using Limma with voom transformation
- A549 SARS_CoV2 vs. Mock_Cov2
- N = 175 significantly changed genes with cut off FDR < 0.05
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Heatmap A549 - Sars_Cov2
Volcano Plot - Sars_Cov2 A549
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DE Stats all genes (A549 SARS_CoV2 vs. Mock_Cov2)
Significanty Upregulated in SAR-CoV2-A549 ( FDR < 0.05)
Significanty Downregulated in SAR-CoV2-A549 ( FDR < 0.05) (A549 SARS_CoV2 vs. Mock_Cov2)
A549 - Pathways
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Pathway analysis summary
GSEA Pathway analysis perforemd on A549 ( MOI 0.2 ) SARS-Cov2 vs. SARS2-Cov2-Mock
Using the Following Databses:
- KEGG (Version 6.2 msigDB)
- REACTOME (Version 6.2 msigDB )
- GO Biological Processes (Version 7 msigDB)
FDR < 0.25
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KEGG Significanty Enriched Pathway Up in A549-SARS_Cov2 ( FDR < 0.25)
KEGG Significanty Enriched Pathway Down in A549-SARS_Cov2 ( FDR < 0.25)
REACTOME - Significanty Enriched Pathway Up in A549-SARS_Cov2 ( FDR < 0.25)
REACTOME - Significanty Enriched Pathway Down in A549-SARS_Cov2 ( FDR < 0.25)
GO Pathways - Significanty Enriched Pathway Up in A549-SARS_Cov2 ( FDR < 0.25)
GO Pathways - Significanty Enriched Pathway Down in A549-SARS_Cov2 ( FDR < 0.25)
NHBE Comparisons
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Differential Expression Analysis
- Using Limma with voom transformation
- SARS_Cov2 NHBE vs. SARS CoV2 MOCK
- N= 252 Signficantly Genes with cut off FDR < 0.05
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Heatmap NHBE - Sars_Cov2
Volcano Plot - Sars_Cov2 NHBE
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DE Stats all genes ( NHBE SARS_CoV2 vs. Mock_Cov2)
Significanty Upregulated genes in SAR-CoV2 NHBE (FDR < 0.05) ( NHBE SARS_CoV2 vs. Mock_Cov2)
Significanty Downregulated genes in SAR-CoV2 NHBE( N=180, FDR < 0.05) ( NHBE SARS_CoV2 vs. Mock_Cov2)
NHBE - Pathways
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Pathway analysis summary
GSEA Pathway analysis perforemd on NHBE SARS-Cov2 ( MOI 2) vs. SARS2-Cov2-Mock
Using the Following Databses:
- KEGG (Version 6.2 msigDB)
- REACTOME (Version 6.2 msigDB )
- GO Biological Processes (Version 7 msigDB)
FDR < 0.25
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KEGG Significanty Enriched Pathway Up in NHBE-SARS_Cov2 ( FDR < 0.25)
KEGG Significanty Enriched Pathway Down in NHBE-SARS_Cov2 ( FDR < 0.25)
REACTOME Significanty Enriched Pathway Up in NHBE-SARS_Cov2 ( FDR < 0.25)
REACTOME Significanty Enriched Pathway Down in NHBE-SARS_Cov2 ( FDR < 0.25)
GO Pathways - Significanty Enriched Pathway Up in NHBE-SARS_Cov2 ( FDR < 0.25)
GO Pathways - Significanty Enriched Pathway Down in NHBE-SARS_Cov2 ( FDR < 0.25)
Overlapping Gene Changes
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Comparing Genes between A549 and NHBE - Sars-Cov2
Analyzed using GeneOverlap
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Heatmap Overlapping Genes in NHBE & A549 - Sars_Cov2
